Hello All,
Let me give you my experience and the steps I've taken to diagnose:

I had my 97 Challenger 1800 out on the lake and it was running fine as always. The port engine sudenly turned off, leaving only the starboard running. I changed the plugs out on the water just to make sure they didn't get fouled, but no luck. I limped the boat back home on one engine (I know this isn't propper, but I wasn't going to paddle an 18 footer 6 miles). I learned that the port engine lacked spark at the plugs. I swapped the 2 ignition coils keeping all wires identical to what they were originally and got the exact same results...port turns over freely put will not start and starboard starts and runs. There is ONLY 2 wires to each ignition coil from the MPEM. 1 positive, 1 negative (x2). I have proven that the coils are fine and NOT the problem, so the only posibility is something BEFORE the coils. This is only 2 very short wires leading directly into the MPEM. I also confirmed compression and fuel presence, so I'm pretty confident that the problem is either the MPEM itself or some other "sensor" feeding info to the MPEM that doesn't allow it to create spark for 1 engine. I have zero direct experience with marine mechanics, but I do have a pretty decent backgroud in automotive backyard mechanics and logical troubleshooting. I am stumped on this one. Any and all help or recommendations will be greatly appreciated.

Lastly, is it "normal" for jet boats to take on some water in the bilge? Or is this indicative of some bad drive shaft seals/bearings on top of my already shotty jet pumps?